Struct FastqChunkStats 

#[non_exhaustive]
pub struct FastqChunkStats {
    pub first_record_index: u64,
    pub records: u64,
    pub bases: u64,
}

Summary for one chunk emitted by FastqReader::next_chunk_with_sink.

Fields (Non-exhaustive)

Non-exhaustive structs could have additional fields added in future. Therefore, non-exhaustive structs cannot be constructed in external crates using the traditional Struct { .. } syntax; cannot be matched against without a wildcard ..; and struct update syntax will not work.

first_record_index: u64

Zero-based index of the first record in this chunk.

records: u64

Number of records emitted into the sink.

bases: u64

Number of sequence bases emitted into the sink.

Implementations

impl FastqChunkStats

pub fn first_record_index(self) -> u64

Zero-based index of the first record in this chunk.

Examples found in repository

examples/fastq_chunk_sink.rs (line 60)

fn main() -> Result<()> {
    let stdin = io::stdin();
    let mut reader = FastqReader::new(stdin.lock());
    let config = FastqChunkConfig::new(10_000_000).min_records(40_000);
    let mut sink = ReadBuffer::default();

    sink.reserve_records(config.estimated_records(150));
    while let Some(stats) = reader.next_chunk_with_sink(config, &mut sink)? {
        let checksum: usize = sink
            .reads
            .iter()
            .map(|read| read.name.len() ^ read.seq.len() ^ read.qual.len())
            .sum();
        eprintln!(
            "chunk first_record={} records={} bases={} checksum={}",
            stats.first_record_index(),
            stats.records(),
            stats.bases(),
            checksum
        );

        // Downstream tools typically hand `sink.reads` to alignment or another
        // processing stage here, then reuse the allocation for the next chunk.
        sink.clear();
        sink.reserve_records(config.estimated_records(150));
    }

    Ok(())
}

pub fn records(self) -> u64

Number of records emitted into the sink.

Examples found in repository

examples/fastq_chunk_sink.rs (line 61)

fn main() -> Result<()> {
    let stdin = io::stdin();
    let mut reader = FastqReader::new(stdin.lock());
    let config = FastqChunkConfig::new(10_000_000).min_records(40_000);
    let mut sink = ReadBuffer::default();

    sink.reserve_records(config.estimated_records(150));
    while let Some(stats) = reader.next_chunk_with_sink(config, &mut sink)? {
        let checksum: usize = sink
            .reads
            .iter()
            .map(|read| read.name.len() ^ read.seq.len() ^ read.qual.len())
            .sum();
        eprintln!(
            "chunk first_record={} records={} bases={} checksum={}",
            stats.first_record_index(),
            stats.records(),
            stats.bases(),
            checksum
        );

        // Downstream tools typically hand `sink.reads` to alignment or another
        // processing stage here, then reuse the allocation for the next chunk.
        sink.clear();
        sink.reserve_records(config.estimated_records(150));
    }

    Ok(())
}

pub fn bases(self) -> u64

Number of sequence bases emitted into the sink.

Examples found in repository

examples/fastq_chunk_sink.rs (line 62)

fn main() -> Result<()> {
    let stdin = io::stdin();
    let mut reader = FastqReader::new(stdin.lock());
    let config = FastqChunkConfig::new(10_000_000).min_records(40_000);
    let mut sink = ReadBuffer::default();

    sink.reserve_records(config.estimated_records(150));
    while let Some(stats) = reader.next_chunk_with_sink(config, &mut sink)? {
        let checksum: usize = sink
            .reads
            .iter()
            .map(|read| read.name.len() ^ read.seq.len() ^ read.qual.len())
            .sum();
        eprintln!(
            "chunk first_record={} records={} bases={} checksum={}",
            stats.first_record_index(),
            stats.records(),
            stats.bases(),
            checksum
        );

        // Downstream tools typically hand `sink.reads` to alignment or another
        // processing stage here, then reuse the allocation for the next chunk.
        sink.clear();
        sink.reserve_records(config.estimated_records(150));
    }

    Ok(())
}

pub fn is_empty(self) -> bool

Whether the chunk contains no records.

Trait Implementations

impl Clone for FastqChunkStats

fn clone(&self) -> FastqChunkStats

Returns a duplicate of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Copy for FastqChunkStats

impl Debug for FastqChunkStats

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl Eq for FastqChunkStats

impl PartialEq for FastqChunkStats

fn eq(&self, other: &FastqChunkStats) -> bool

Tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

Tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl StructuralPartialEq for FastqChunkStats